7WWQ: Human Ufd1-Npl4 complex

Crystal structure of human Ufd1-Npl4 complex. Determined by X-ray diffraction at 2.72 Å resolution. Released 21 Sept 2022.

Method: X-ray diffraction
Resolution: 2.72 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,273
Mol. weight: 54.76 kDa
Released: 21 Sept 2022

Explore 7WWQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7WWQ contains 16 α-helices and 25 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	109-114	6
α-helix	151-153	3
β-strand	162-163	2	1
α-helix	164-169	6
β-strand	215	1	2
β-strand	220-221	2	1
β-strand	225-228	4	3
α-helix	231-244	14
β-strand	249-259	11	3
β-strand	265-274	10	3
β-strand	278-281	4	4
β-strand	284-287	4	4
α-helix	293-302	10
β-strand	306-313	8	3
β-strand	317	1	5
β-strand	325	1	5
α-helix	338-350	13
β-strand	352-354	3	6
β-strand	362-365	4	6
β-strand	368-374	7	3
β-strand	380-387	8	3
α-helix	389-396	8
β-strand	400-401	2	7
β-strand	409-410	2	8
β-strand	411-412	2	7
β-strand	425-426	2	2
β-strand	429	1	9
β-strand	435	1	9
β-strand	438-439	2	2
β-strand	443-444	2	8
α-helix	445-447	3
β-strand	449-455	7	3
α-helix	470-473	4
α-helix	477-479	3
α-helix	485-494	10
α-helix	500-504	5
α-helix	507-515	9
α-helix	526-533	8
α-helix	537-544	8
α-helix	547-556	10

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	267-269	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear protein localization protein 4 homolog	A	protein	465	Homo sapiens	Q8TAT6 (AlphaFold model)
Ubiquitin recognition factor in ER-associated degradation protein 1	B	protein	16	Homo sapiens	Q92890 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7WWQ_1 Nuclear protein localization protein 4 homolog (chains A)
GFKVFGAPNVVEDEIDQYLSKQDGKIYRSRDPQLCRHGPLGKCVHCVPLEPFDEDYLNHL
EPPVKHMSFHAYIRKLTGGADKGKFVALENISCKIKSGCEGHLPWPNGICTKCQPSAITL
NRQKYRHVDNIMFENHTVADRFLDFWRKTGNQHFGYLYGRYTEHKDIPLGIRAEVAAIYE
PPQIGTQNSLELLEDPKAEVVDEIAAKLGLRKVGWIFTDLVSEDTRKGTVRYSRNKDTYF
LSSEECITAGDFQNKHPNMCRLSPDGHFGSKFVTAVATGGPDNQVHFEGYQVSNQCMALV
RDECLLPCKDAPELGYAKESSSEQYVPDVFYKDVDKFGNEITQLARPLPVEYLIIDITTT
FPKDPVYTFSISQNPFPIENRDVLGETQDFHSLATYLSQNTSSVFLDTISDFHLLLFLVT
NEVMPLQDSISLLLEAVRTRNEELAQTWKRSEQWATIEQLCSTVG

Sequence of entity 2 (B), FASTA

>7WWQ_2 Ubiquitin recognition factor in ER-associated degradation protein 1 (chains B)
IPNYEFKLGKITFIRN

Primary citation

Structural basis for the interaction between human Npl4 and Npl4-binding motif of human Ufd1. Nguyen, T.Q., My Le, L.T., Kim, D.H. et al. Structure (2022) 30:1530-1537.e3. DOI 10.1016/j.str.2022.08.005 · PubMed

Other PDB entries of the same protein (UniProt Q8TAT6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9YRC 2.97 Å, p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
7WWP 2.99 Å, Crystal structure of human Npl4
11TA 3.58 Å, Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused)
11VE 3.85 Å, Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (State1)
11SY 4.28 Å, Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused)

Browse structure collections

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